arXiv subjects

Chantal Valeriani

Publications and source records attributed to Chantal Valeriani.

At least 55 records · Page 3Linked to original sources

arXiv2022

Dynamical anomalies and structural features of Active Brownian Particles characterised by two repulsive length scales

In this work we study a two-dimensional system composed by Active Brownian Particles (ABPs) interacting via a repulsive potential with two-length-scales, a soft shell and a hard-core. Depending on the ratio between the strength of the soft shell barrier and the activity, we find two regimes: If this ratio is much larger or smaller than 1, the observed behaviour is comparable with ABPs interacting via a single length-scale potential. If this ratio is similar to 1, the two length-scales are relevant for both structure and dynamical properties. On the structural side, when the system exhibits a motility induced phase separation, the dense phase is characterised by new and more complex structures compared with the hexatic phase observed in single length-scale systems. On the dynamical side, as far as we are aware, this is the first representation of an anomalous dynamics in active particles.

cond-mat.soft↗

arXiv2022

Intrinsic structure perspective for MIPS interfaces in two dimensional systems of Active Brownian Particles

Suspensions of Active Brownian Particles (ABP) undergo motility induced phase separation (MIPS) over a wide range of mean density and activity strength [1], even in the absence of an explicit attraction. Negative values of the mechanical surface tension have been reported, from the total forces across the interface, while the stable fluctuations of the interfacial line would be interpreted as a positive capillary surface tension [2], while in equilibrium liquid surfaces these two magnitudes are equal. We present here the analysis of 2D-ABP interfaces in terms of the intrinsic density and force profiles, calculated with the particle distance to the instantaneous interfacial line. Our results provide a new insight in the origin of the MIPS from the local rectification of the random active force on the particles near the interface. As it had been pointed, that effect acts as an external potential [3] that produces a pressure gradient across the interface, so that the mechanical surface tension of the MIPS cannot be described as that of equilibrium coexisting phases; but our analysis shows that most of that effect comes from the tightly caged particles at the dense (inner) side of the MIPS interface, rather than from the free moving particles at the outer side that collide with the dense cluster. Moreover, a clear correlation appears between the decay of the hexatic order parameter at the dense slab and the end of the MIPS as the strength of the active force is lowered. We test that with the strong active forces required for MIPS, the interfacial structure and properties are very similar for ABP with purely repulsive (WCA-LJ model truncated at its minimum) and when the interaction includes a range of the LJ attractive force.

cond-mat.soft↗

arXiv2021

Influence of water models on water movement through AQP1

Water diffusion through membrane proteins is a key aspect of cellular function. Essential processes of cellular metabolism are driven by osmotic pressure, which depends on water channels. Membrane proteins such as aquaporins (AQPs) are responsible for enabling water transport through the cell membrane. AQPs are highly selective, allowing only water and relatively small polar molecules to cross the membrane. Experimentally, estimation of water flux through membrane proteins is still a challenge, and hence accurate simulations of water transport are of particular importance. We present a numerical study of water diffusion through AQP1 comparing three water models: TIP3P, OPC and TIP4P/2005. Bulk diffusion, diffusion permeability and osmotic permeability are computed and compared among all models. The results show that there are significant differences between TIP3P (a particularly widespread model for simulations of biological systems), and the more recently developed TIP4P/2005 and OPC models. We demonstrate that OPC and TIP4P/2005 reproduce protein-water interactions and dynamics in excellent agreement with experimental data. From this study, we find that the choice of the water model has a significant effect on the computed water dynamics as well as its molecular behaviour within a biological nanopore.

cond-mat.soft↗

arXiv2021

Collective motion of run-and-tumble particles drives aggregation in one-dimensional systems

Active matter deals with systems whose particles consume energy at the individual level in order to move. To unravel features such as the emergence of collective structures several models have been suggested, such as the on-lattice model of run-and-tumble particles implemented via the Persistent Exclusion Process (PEP). In our work, we study a one dimensional system of run-and-tumble repulsive or attractive particles, both on and off lattice. Additionally, we implement a cluster motility dynamics in the on-lattice case (since in the off-lattice case cluster motility arises from the individual particle dynamics). While we observe important differences between discrete and continuous dynamics, few common features are of particular importance. Increasing particle density drives aggregation across all different systems explored. For non-attractive particles, the effects of particle activity on aggregation are largely independent of the details of the dynamics. On the contrary, once attractive interactions are introduced, the steady state, which is completely determined by the interplay between these and the particles' activity, becomes highly dependent on the details of the dynamics.

cond-mat.soft↗

arXiv2021

Heterogeneous versus homogeneous crystal nucleation in hard spheres

Hard-sphere model systems are well-suited in both experiment and simulations to investigate fundamental aspects of the crystallization of fluids. In experiments on colloidal models of hard-sphere fluids, the uid is unavoidably at contact with the walls of the sample cell, where heterogeneous crystallization may take place. In this work we use simulations to investigate the competition between homogeneous and heterogeneous crystallization. We report simulations of wall-induced nucleation for different confining walls. Combining the results of these simulations with earlier studies of homogeneous allows us to asses the competition between homogeneous and heterogeneous nucleation as a function of wall type, fluid density and the system size. On at walls, heterogeneous nucleation will typically overwhelm homogeneous nucleation. However, even for surfaces randomly coated with spheres with a diameter that was some three times larger than that of the fluid spheres - as has been used in some experiments - heterogeneous nucleation is likely to be dominant for volume fractions smaller than 0.535. Only for a disordered coating that has the same structure as the liquid holds promise did we find the nucleation was likely to occur in the bulk. Hence, such coatings might be used to suppress heterogeneous nucleation in experiments. Finally, we report the apparent homogeneous nucleation rate taking into account the formation of crystallites both in the bulk and at the walls. We find that the apparent overall nucleation rates coincides with those reported in "homogeneous nucleation" experiments. This suggests that heterogeneous nucleation at the walls could partly explain the large discrepancies found between experimental measurements and simulation estimates of the homogeneous nucleation rate.

cond-mat.soft↗

arXiv2021

Characterization of MIPS in a suspension of repulsive Active Brownian Particles through dynamical features

The two-dimensional Active Brownian Particles system is meant to be composed of hard disks, that show excluded volume interactions, usually simulated via molecular dynamics using pure repulsive potentials. We show that the softness of the chosen potential plays a role in the result of the simulation, focusing on the case of the emergence of Motility Induced Phase Separation. In a pure hard-sphere system with no traslational diffusion,the phase diagram should be completely determined by their density and Péclet number. However, we have found two additional effects that affect the phase diagram in the ABP model we simulate: the relative strength of the traslational diffusion compared to the propulsion term and the overlapping of the particles. As we show, the second effect can be strongly mitigated if we use, instead of the standard Weeks-Chandler- Andersen potential, a harder one, the pseudo-hard spheres potential. Moreover, in determining the boundary of our phase space, we have tried different approaches to detect MIPS and concluded that observing dynamical features, via the non-Gaussian parameter, is more efficient than observing structural ones, via the local density distribution function. We also demonstrate that the Vogel-Fulcher equation successfully reproduces the decay of the diffusion as a function of density, except for very high density cases. Thus, the ABP system behaves similarly to a fragile glass in this regard.

cond-mat.soft↗

arXiv2021

In-silico modeling of early-stage biofilm formation

Several bacteria and bacteria strands form biofilms in different environmental conditions, e.g. pH, temperature, nutrients, etc. Biofilm growth, therefore, is an extremely robust process. Because of this, while biofilm growth is a complex process affected by several variables, insights into biofilm formation could be obtained studying simple schematic models. In this manuscript, we describe a hybrid molecular dynamics and Monte Carlo model for the simulation of the early stage formation of a biofilm, to explicitly demonstrate that it is possible to account for most of the processes expected to be relevant. The simulations account for the growth and reproduction of the bacteria, for their interaction and motility, for the synthesis of extracellular polymeric substances and Psl trails. We describe the effect of these processes on the early stage formation of biofilms, in two dimensions, and also discuss preliminary three-dimensional results.

cond-mat.soft↗

arXiv2021

Self-adaptation of Pseudomonas fluorescens biofilms to hydrodynamic stress

In some conditions, bacteria self-organise into biofilms, supracellular structures made of a self-produced embedding matrix, mainly composed on polysaccharides, DNA, proteins and lipids. It is known that bacteria change their colony/matrix ratio in the presence of external stimuli such as hydrodynamic stress. However, little is still known about the molecular mechanisms driving this self-adaptation. In this work, we monitor structural features of Pseudomonas fluorescens biofilms grown with and without hydrodynamic stress. Our measurements show that the hydrodynamic stress concomitantly increases the cell density population and the matrix production. At short growth timescales, the matrix mediates a weak cell-cell attractive interaction due to the depletion forces originated by the polymer constituents. Using a population dynamics model, we conclude that hydrodynamic stress causes a faster diffusion of nutrients and a higher incorporation of planktonic bacteria to the already formed microcolonies. This results in the formation of more mechanically stable biofilms due to an increase of the number of crosslinks, as shown by computer simulations. The mechanical stability also lies on a change in the chemical compositions of the matrix, which becomes enriched in carbohydrates, known to display adhering properties. Overall, we demonstrate that bacteria are capable of self-adapting to hostile hydrodynamic stress by tailoring the biofilm chemical composition, thus affecting both the mesoscale structure of the matrix and its viscoelastic properties that ultimately regulate the bacteria-polymer interactions.

cond-mat.soft↗

arXiv2020

Effect of dissolved salt on the anomalies of water at negative pressure

Adding salt to water at ambient pressure affects its thermodynamic properties. At low salt concentration, anomalies such as the density maximum are shifted to lower temperature, while at large enough salt concentration they cannot be observed any more. Here we investigate the effect of salt on an anomaly recently observed in pure water at negative pressure: the existence of a sound velocity minimum along isochores. We compare experiments and simulations for an aqueous solution of sodium chloride with molality around $1.2\,\mathrm{mol\,kg^{-1}}$, reaching pressures beyond $-100\,\mathrm{MPa}$. We also discuss the origin of the minima in the sound velocity and emphasize the importance of the relative position of the temperatures of sound velocity and density anomalies.

physics.chem-ph↗

arXiv2020

Seeding Approach to Bubble Nucleation in Superheated Lennard Jones Fluids

We investigate vapor homogeneous nucleation in a superheated Lennard Jones liquid with computer simulations. Special simulation techniques are required to address this study since the nucleation of a critical vapor bubble --one that has equal chance to grow or shrink-- in a moderately superheated liquid is a rare event. We use the Seeding method, that combines Classical Nucleation Theory with computer simulations of a liquid containing a vapor bubble to provide bubble nucleation rates in a wide temperature range. Seeding has been successfully applied to investigate the nucleation of crystals in supercooled fluids and here we apply it for the fist time --to the best of our knowledge-- to the liquid-to-vapor transition. We find that Seeding provides nucleation rates that are consistent with independent calculations not based on the assumptions of Classical Nucleation Theory. Different criteria to determine the radius of the critical bubble give different rate values. The accuracy of each criterion depends of the degree of superheating. Moreover, Seeding simulations show that the surface tension depends on pressure for a given temperature. Therefore, using Classical Nucleation Theory with the coexistence surface tension does not provide good estimates of the nucleation rate.

cond-mat.soft↗

arXiv2020

Seeding Approach to nucleation in the NVT ensemble: the case of bubble cavitation in overstretched Lennard Jones fluids

Simulations are widely used to study nucleation in first order phase transitions due to the fact that they have access to the relevant length and time scales. However, simulations face the problem that nucleation is an activated process. Therefore, rare event simulation techniques are needed to promote the formation of the critical nucleus. The Seeding method, where the simulations are started with the nucleus already formed, has proven quite useful in efficiently providing estimates of the nucleation rate for a wide range of orders of magnitude. So far, Seeding has been employed in the NPT ensemble, where the nucleus either grows or redissolves. Thus, several trajectories have to be run in order to find the thermodynamic conditions that make the seeded nucleus critical. Moreover, the nucleus lifetime is short and the statistics for obtaining its properties is consequently poor. To deal with these shortcomings we extend the Seeding method to the NVT ensemble. We focus on the problem of bubble nucleation in a mestastable Lennard Jones fluid. We show that, in the NVT ensemble, it is possible to equilibrate and stabilise critical bubbles for a long time. The nucleation rate inferred from NVT-Seeding is fully consistent with that coming from NPT-Seeding. The former is quite suitable to obtain the nucleation rate along isotherms, whereas the latter is preferable if the dependence of the rate with temperature at constant pressure is required. Care should be taken with finite size effects when using NVT-Seeding. Further work is required to extend NVT seeding to other sorts of phase transitions.

cond-mat.soft↗

arXiv2019

Trapping flocking particles with asymmetric obstacles

Asymmetric obstacles can be exploited to direct the motion and induce sorting of run-and-tumbling particles. In this work, we show that flocking particles which follow the Vicsek model aligning rules experience a collective trapping in the presence of a wall of funnels made of chevrons, concentrating at the opposite side of a wall of funnels than run-and-tumbling particles. Flocking particles can be completely trapped or exhibit a dynamical trapping behaviour; these two regimes open the door to the design of a system with two perpendicular flows of active particles. This systematic study broaden our understanding about the emergence of collective motion of microorganisms in confined environments and direct the design of new microfluidics devices able to controlthese collective behaviours.

cond-mat.soft↗

arXiv2019

Collective behavior of Vicsek particles without and with obstacles

In our work we have studied a two-dimensional suspension of finite-size Vicsek hard-disks, whose time evolution follows an event-driven dynamics between subsequent time steps. Having compared its collective behaviour with the one expected for a system of scalar Vicsek point-like particles, we have analysed the effect of considering two possible bouncing rules between the disks: a Vicsek-like rule and a pseudo-elastic one, focusing on the order-disorder transition. Next, we have added to the two-dimensional suspension of hard-disk Vicsek particles disk-like passive obstacles of two types: either fixed in space or moving according to the same event-driven dynamics. We have performed a detailed analysis of the particles' collective behaviour observed for both fixed and moving obstacles. In the fixed obstacles case, we have observed formation of clusters at low noise, in agreement with previous studies. When using moving passive obstacles, we found that that order of active particles is better destroyed as the drag of obstacles increases. In the no drag limit an interesting result was found: introduction of low drag passive particles can lead in some cases to a more ordered state of active flocking particles than what they show in bulk.

cond-mat.soft↗

arXiv2019

Orientational order and morphology of clusters of self-assembled Janus swimmers

Due to the combined effect of anisotropic interactions and activity, Janus swimmers are capable to self-assemble in a wide variety of structures, many more than their equilibrium counterpart. This might lead to the development of novel active materials capable of performing tasks without any central control. Their potential application in designing such materials endows trying to understand the fundamental mechanism in which these swimmers self-assemble. In the present work, we study a quasi-two dimensional semi-dilute suspensions of two classes of amphiphilic spherical swimmers whose direction of motion can be tuned: either swimmers propelling in the direction of the hydrophobic patch (WP), or swimmers propelling in the opposite direction (towards the hydrophilic side) (AP). In both systems we have systematically tuned swimmers' hydrophobic strength and signature, and observed that the anisotropic interactions, characterized by the angular attractive potential and its interaction range, in competition with the active stress, pointing towards or against the attractive patch gives rise to a rich aggregation phenomenology.

cond-mat.soft↗

arXiv2018

Viscosity and self-diffusion of supercooled and stretched water from molecular dynamics simulations

Among the numerous anomalies of water, the acceleration of dynamics under pressure is particularly puzzling. Whereas the diffusivity anomaly observed in experiments has been reproduced in several computer studies, the parallel viscosity anomaly has received less attention. Here we simulate viscosity and self-diffusion coefficient of the TIP4P/2005 water model over a broad temperature and pressure range. We reproduce the experimental behavior, and find additional anomalies at negative pressure. The anomalous effect of pressure on dynamic properties becomes more pronounced upon cooling, reaching two orders of magnitude for viscosity at 220 K. We analyze our results with a dynamic extension of a thermodynamic two-state model, an approach which has proved successful in describing experimental data. Water is regarded as a mixture of interconverting species with contrasting dynamic behaviors, one being strong (Arrhenius), and the other fragile (non-Arrhenius). The dynamic parameters of the two-state models are remarkably close between experiment and simulations. The larger pressure range accessible to simulations suggests a modification of the dynamic two-state model, which in turn also improves the agreement with experimental data. Furthermore, our simulations demonstrate the decoupling between viscosity $η$ and self-diffusion coefficient $D$ as a function of temperature $T$. The Stokes-Einstein relation, which predicts a constant $D η/T$, is violated when $T$ is lowered, in connection with the Widom line defined by an equal fraction of the two interconverting species. These results provide a unifying picture of thermodynamics and dynamics in water, and call for experiments at negative pressure.

physics.chem-ph↗

arXiv2018

Phase boundaries, nucleation rates and speed of crystal growth of the water-to-ice transition under an electric field: a simulation study

We investigate with computer simulations the effect of applying an electric field on the water-to-ice transition. We use a combination of state-of-the-art simulation techniques to obtain phase boundaries and crystal growth rates (direct coexistence), nucleation rates (seeding) and interfacial free energies (seeding and mold integration). First, we consider ice Ih, the most stable polymorph in the absence of a field. Its normal melting temperature, speed of crystal growth and nucleation rate (for a given supercooling) diminish as the intensity of the field goes up. Then, we study polarised cubic ice, or ice Icf, the most stable solid phase under a strong electric field. Its normal melting point goes up with the field and, for a given supercooling, under the studied field (0.3 V/nm) ice Icf nucleates and grows at a similar rate as Ih with no field. The net effect of the field would be then that ice nucleates at warmer temperatures, but in the form of ice Icf. The main conclusion of this work is that reasonable electric fields (not strong enough to break water molecules apart) are not relevant in the context of homogeneous ice nucleation at 1 bar.

cond-mat.soft↗

arXiv2017

Two-structure thermodynamics for the TIP4P/2005 model of water covering supercooled and deeply stretched regions

One of the most promising frameworks for understanding the anomalies of cold and supercooled water postulates the existence of two competing, interconvertible local structures. If the non-ideality in the Gibbs energy of mixing overcomes the ideal entropy of mixing of these two structures, a liquid-liquid phase transition, terminated at a liquid-liquid critical point, is predicted. Various versions of the "two-structure equation of state" (TSEOS) based on this concept have shown remarkable agreement with both experimental data for metastable, deeply supercooled water and simulations of molecular water models. However, existing TSEOSs were not designed to describe the negative pressure region and do not account for the stability limit of the liquid state with respect to the vapor. While experimental data on supercooled water at negative pressures may shed additional light on the source of the anomalies of water, such data are very limited. To fill this gap, we have analyzed simulation results for TIP4P/2005, one of the most accurate classical water models available. We have used recently published simulation data, and performed additional simulations, over a broad range of positive and negative pressures, from ambient temperature to deeply supercooled conditions. We show that, by explicitly incorporating the liquid-vapor spinodal into a TSEOS, we are able to match the simulation data for TIP4P/2005 with remarkable accuracy. In particular, this equation of state quantitatively reproduces the lines of extrema in density, isothermal compressibility, and isobaric heat capacity. Contrary to an explanation of the thermodynamic anomalies of water based on a "retracing spinodal", the liquid-vapor spinodal in the present TSEOS continues monotonically to lower pressures upon cooling, influencing but not giving rise to density extrema and other thermodynamic anomalies.

cond-mat.stat-mech↗

arXiv2017

A simulation study of homogeneous ice nucleation in supercooled salty water

We use computer simulations to investigate the effect of salt on homogeneous ice nucleation. The melting point of the employed solution model was obtained both by direct coexistence simulations and by thermodynamic integration from previous calculations of the water chemical potential. Using a Seeding approach, in which we simulate ice seeds embedded in a supercooled aqueous solution, we compute the nucleation rate as a function of temperature for a 1.85 NaCl mole per water kilogram solution at 1 bar. To improve the accuracy and reliability of our calculations we combine Seeding with the direct computation of the ice-solution interfacial free energy at coexistence using the Mold Integration method. We compare the results with previous simulation work on pure water to understand the effect caused by the solute. The model captures the experimental trend that the nucleation rate at a given supercooling decreases when adding salt. Despite the fact that the thermodynamic driving force for ice nucleation is higher for salty water for a given supercooling, the nucleation rate slows down with salt due to a significant increase of the ice-fluid interfacial free energy. The salty water model predicts an ice nucleation rate that is in good agreement with experimental measurements, bringing confidence in the predictive ability of the model.

cond-mat.soft↗